Protein–Ligand Docking with Evolutionary Algorithms

2007 ◽  
pp. 167-195 ◽  
Author(s):  
Ren Thomsen
Keyword(s):  
Evolutionary Algorithms ◽  
Ligand Docking

Opponent Center-Surround Contrast: Colour to Grey Conversion

2020 ◽  
Vol 2020 (1) ◽  
pp. 105-108
Author(s):  
Ali Alsam
Keyword(s):  
Evolutionary Algorithms ◽  
Three Dimensional ◽  
The State ◽  
Colour Space ◽  
Vision Science ◽  
State Of Art ◽  
Over Time

Vision is the science that informs us about the biological and evolutionary algorithms that our eyes, opticnerves and brains have chosen over time to see. This article is an attempt to solve the problem of colour to grey conversion, by borrowing ideas from vision science. We introduce an algorithm that measures contrast along the opponent colour directions and use the results to combine a three dimensional colour space into a grey. The results indicate that the proposed algorithm competes with the state of art algorithms.

Evaluation of Grey Wolf Optimization Algorithm on Rigid and Flexible Receptor Docking

2020 ◽  
Author(s):  
Kin Meng Wong ◽  
Shirley Siu
Keyword(s):  
Scoring Function ◽  
Ligand Docking ◽  
Receptor Protein ◽  
Pose Prediction ◽  
Grey Wolf ◽  
Success Rates ◽  
Autodock Vina ◽  
Grey Wolf Optimization ◽  
Structure Based Drug Design ◽  
Docking Program

Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein in current structure-based drug design. In this paper, we evaluate the performance of grey wolf optimization (GWO) in protein-ligand docking. Two versions of the GWO docking program – the original GWO and the modified one with random walk – were implemented based on AutoDock Vina. Our rigid docking experiments show that the GWO programs have enhanced exploration capability leading to significant speedup in the search while maintaining comparable binding pose prediction accuracy to AutoDock Vina. For flexible receptor docking, the GWO methods are competitive in pose ranking but lower in success rates than AutoDockFR. Successful redocking of all the flexible cases to their holo structures reveals that inaccurate scoring function and lack of proper treatment of backbone are the major causes of docking failures.

Applied Process Simulation-Driven Oil and Gas Separation Plant Optimization using Surrogate Modeling and Evolutionary Algorithms

2019 ◽  
Author(s):  
Anders Andreasen
Keyword(s):  
Evolutionary Algorithms ◽  
Gas Separation ◽  
Oil And Gas ◽  
Optimal Solution ◽  
Computer Experiment ◽  
Latin Hypercube Sampling ◽  
Surrogate Models ◽  
Inlet Temperature ◽  
Separation Plant ◽  
Separation Stage

In this article the optimization of a realistic oil and gas separation plant has been studied. Two different fluids are investigated and compared in terms of the optimization potential. Using Design of Computer Experiment (DACE) via Latin Hypercube Sampling (LHS) and rigorous process simulations, surrogate models using Kriging have been established for selected model responses. The surrogate models are used in combination with a variety of different evolutionary algorithms for optimizing the operating profit, mainly by maximizing the recoverable oil production. A total of 10 variables representing pressure and temperature various key places in the separation plant are optimized to maximize the operational profit. The optimization is bounded in the variables and a constraint function is included to ensure that the optimal solution allows export of oil with an RVP < 12 psia. The main finding is that, while a high pressure is preferred in the first separation stage, apparently a single optimal setting for the pressure in downstream separators does not appear to exist. In the second stage separator apparently two different, yet equally optimal, settings are revealed. In the third and final separation stage a correlation between the separator pressure and the applied inlet temperature exists, where different combinations of pressure and temperature yields equally optimal results.<br>

Convergence Analysis and Comparison of Evolutionary Algorithms Based on Relation Model

2011 ◽  
Vol 34 (5) ◽  
pp. 801-811 ◽  
Author(s):  
Han HUANG ◽  
Zhi-Yong LIN ◽  
Zhi-Feng HAO ◽  
Yu-Shan ZHANG ◽  
Xue-Qiang LI
Keyword(s):  
Evolutionary Algorithms ◽  
Convergence Analysis ◽  
Relation Model
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